PDCD11

programmed cell death 11, the group of Minor histocompatibility antigens|SSU processome

Basic information

Region (hg38): 10:103396625-103446294

Links

ENSG00000148843 ∙ NCBI:22984 ∙ OMIM:612333 ∙ HGNC:13408 ∙ Uniprot:Q14690 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDCD11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD11 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			99	6		105
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	99	9	0

Variants in PDCD11

This is a list of pathogenic ClinVar variants found in the PDCD11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-103398431-C-T		not specified	Uncertain significance (Jan 27, 2022)
10-103400465-G-A			Likely benign (Mar 01, 2023)
10-103400470-T-C		not specified	Uncertain significance (Jan 05, 2022)
10-103400496-G-A		not specified	Uncertain significance (Mar 15, 2024)
10-103403136-C-T		not specified	Uncertain significance (Oct 12, 2021)
10-103403176-T-C		not specified	Uncertain significance (Mar 13, 2023)
10-103403194-A-G		not specified	Uncertain significance (May 26, 2024)
10-103406079-C-T		not specified	Uncertain significance (May 10, 2023)
10-103406104-C-G		not specified	Uncertain significance (May 11, 2022)
10-103406667-C-T			Likely benign (Oct 01, 2022)
10-103406680-A-T		not specified	Uncertain significance (Mar 28, 2023)
10-103406744-T-C		not specified	Uncertain significance (Jun 04, 2024)
10-103406759-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-103409718-C-T		not specified	Uncertain significance (Feb 17, 2022)
10-103409747-G-A		not specified	Uncertain significance (Dec 21, 2022)
10-103409748-T-A		not specified	Uncertain significance (Oct 13, 2023)
10-103413147-G-C		not specified	Uncertain significance (May 04, 2023)
10-103413152-A-G		not specified	Uncertain significance (Mar 31, 2024)
10-103413161-C-A		not specified	Uncertain significance (Sep 16, 2021)
10-103413174-G-A		not specified	Uncertain significance (Apr 28, 2023)
10-103413209-C-G		not specified	Uncertain significance (Nov 12, 2021)
10-103413243-A-G		not specified	Uncertain significance (Jun 02, 2023)
10-103413245-G-A		not specified	Uncertain significance (Nov 30, 2021)
10-103413297-A-C		not specified	Uncertain significance (Feb 17, 2022)
10-103413320-C-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD11	protein_coding	protein_coding	ENST00000369797	35	49645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.29e-16	1.00	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	943	1.04e+3	0.903	0.0000597	12189
Missense in Polyphen		284	318.97	0.89038		3701
Synonymous	1.92	385	436	0.883	0.0000266	3754
Loss of Function	4.79	42	91.4	0.459	0.00000527	1056

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000850	0.000844
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000409	0.000404
Middle Eastern	0.000272	0.000272
South Asian	0.000296	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. {ECO:0000269|PubMed:17654514}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.682
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.18

Haploinsufficiency Scores

• pHI: 0.0497
• hipred: Y
• hipred_score: 0.637
• ghis: 0.585

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pdcd11

Gene ontology

• Biological process: rRNA processing;mRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;small-subunit processome
• Molecular function: RNA binding;protein binding;transcription factor binding